BACKGROUND: Differences in the distribution of the MTRR rs326119 polymorphism (c.56 + 781 A > C) between patients with congenital heart disease (CHD) and controls have been described in Chinese individuals. The association is thought to be due to deregulation of homocysteine-cobalamin pathways. This has not been replicated in other populations. The primary objective of this study was to assess the influence of the MTRR rs326119 polymorphism on biochemical parameters of vitamin B12 metabolism, coronary lesions, and congenital heart disease in Brazilian subjects. METHODS: We selected 722 patients with CHD, 1432 patients who underwent coronary angiography, and 156 blood donors. Genotyping for the MTRR polymorphism was evaluated by high-resolution melting analysis, and biochemical tests of vitamin B12 metabolism were measured. RESULTS: Subjects carrying the AC or CC genotypes had higher homocysteine concentrations (9.7 ± 0.4 µmol/L and 10.1 ± 0.6 µmol/L) and lower cobalamin concentrations (260.5 ± 13.3 pmol/L and 275.6 ± 19.9 pmol/L) compared with the subjects carrying the AA genotype (8.7 ± 0.5 µmol/L and 304.8 ± 14.7 pmol/L), respectively. A multiple linear regression model also identified a significant association between the number of C variant alleles with the concentrations of homocysteine and cobalamin. Nonetheless, the allelic and genotypic distributions for MTRR rs326119 were not associated with CHD or coronary atherosclerosis in the studied samples. CONCLUSION: Our findings indicate that the MTRR rs326119 variant might be a genetic marker associated with homocysteine and cobalamin concentrations, but not a strong risk factor for CHD or coronary atherosclerosis in the Brazilian population.